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Abstract We study the stability and nonlinear local dynamics of spectrally stable periodic wave trains of the Korteweg‐de Vries/Kuramoto‐Sivashinsky equation when subjected to classes of periodic perturbations. It is known that for each, such a‐periodic wave train is asymptotically stable to‐periodic, i.e., subharmonic, perturbations, in the sense that initially nearby data will converge asymptotically to a small Galilean boost of the underlying wave, with exponential rates of decay. However, both the allowable size of initial perturbations and the exponential rates of decay depend onand, in fact, tend to zero as, leading to a lack of uniformity in such subharmonic stability results. Our goal here is to build upon a recent methodology introduced by the authors in the reaction–diffusion setting and achieve a subharmonic stability result, which is uniform in. This work is motivated by the dynamics of such wave trains when subjected to perturbations that are localized (i.e., integrable on the line).
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Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields
Abstract The potentials of mean force (PMFs) along the end‐to‐end distance of two different helical peptides have been obtained and benchmarked using the adaptive steered molecular dynamics (ASMD) method. The results depend strongly on the choice of force field driving the underlying all‐atom molecular dynamics, and are reported with respect to the three most popular CHARMM force field versions: c22, c27 and c36. Two small peptides,and 1PEF, serve as the particular case studies. The comparisons between the versions of the CHARMM force fields provides both a qualitative and quantitative look at their performance in forced unfolding simulations in which peptides undergo large changes in structural conformations. We find that ASMD with the underlying c36 force field provides the most robust results for the selected benchmark peptides.
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- Award ID(s):
- 2102455
- PAR ID:
- 10370711
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- ChemPhysChem
- Volume:
- 23
- Issue:
- 17
- ISSN:
- 1439-4235
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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